Last summer, I let mine sit in the garage for a few days with the top in the down position (I don't usually do this).
Ever since, it has folded correctly every time.
I haven't had the top down since autumn, so I'm not sure if it stayed "trained".
I've never had to do the boxster chop - and I regularly leave mine down for several days at a time without raising it. Maybe you're on to the best solution, Particlewave.